Bottom Line:
A significantly high level of sequence conservation was detected in three regions on each genome.An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements.The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

ABSTRACTThe complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

f1-genes-02-00763: Schematic representations of circular replicons in B. japonicum strains. (a) USDA6T chromosome and (b) USDA110. The scale towards the outside of each map indicates genomic location (in kb). The bars in the outermost circle and the second circle show the positions of the putative protein-encoding genes in clockwise and counter-clockwise directions, respectively. The putative genes are represented by 18 colors, based on Clusters of Orthologous Groups (COG) assignments, as described in Supplemental Figure 1. The third circle from the outside indicates positions of structural RNA genes. In the fourth circle, the black bars indicate areas of putative genomic islands inserted in a tRNA gene. Three red bars within the fifth circle represent regions corresponding to the possible symbiosis island. The sixth circle shows the distribution of insertion sequences (ISs), as black bars. The innermost and second circles from the center show the GC skew values (yellow and purple) and the average GC percentage (blue and red), respectively, calculated using a window-size of 10 kb. This map was depicted using the GenomeViz program.

Mentions:
The chromosome of B. japonicum USDA6T is a circular molecule of 9,207,384 bp with an average GC content of 63.67% (Table 2, Figure 1a). No plasmid was detected during the course of this study, including in PFGE patterns. Nucleotide position was assigned as corresponding to the nucleotide sequence initiation site of the B. japonicum USDA110 chromosome [5]. Briefly, numbering began at one of the recognition sites of the restriction enzyme Pac I (TTAATTAA). Hypothetical PmeI and SwaI restriction patterns were calculated for the genome sequence of USDA6T, whose size was fixed at 9,207 kb. The restriction patterns are shown in Table 1. The resulting eight fragments, from 103 kb to 2,322 kb, roughly corresponded to the physical restriction patterns of the total DNA seen in PFGE analysis. This supports the structural integrity of the complete genome sequence.

f1-genes-02-00763: Schematic representations of circular replicons in B. japonicum strains. (a) USDA6T chromosome and (b) USDA110. The scale towards the outside of each map indicates genomic location (in kb). The bars in the outermost circle and the second circle show the positions of the putative protein-encoding genes in clockwise and counter-clockwise directions, respectively. The putative genes are represented by 18 colors, based on Clusters of Orthologous Groups (COG) assignments, as described in Supplemental Figure 1. The third circle from the outside indicates positions of structural RNA genes. In the fourth circle, the black bars indicate areas of putative genomic islands inserted in a tRNA gene. Three red bars within the fifth circle represent regions corresponding to the possible symbiosis island. The sixth circle shows the distribution of insertion sequences (ISs), as black bars. The innermost and second circles from the center show the GC skew values (yellow and purple) and the average GC percentage (blue and red), respectively, calculated using a window-size of 10 kb. This map was depicted using the GenomeViz program.

Mentions:
The chromosome of B. japonicum USDA6T is a circular molecule of 9,207,384 bp with an average GC content of 63.67% (Table 2, Figure 1a). No plasmid was detected during the course of this study, including in PFGE patterns. Nucleotide position was assigned as corresponding to the nucleotide sequence initiation site of the B. japonicum USDA110 chromosome [5]. Briefly, numbering began at one of the recognition sites of the restriction enzyme Pac I (TTAATTAA). Hypothetical PmeI and SwaI restriction patterns were calculated for the genome sequence of USDA6T, whose size was fixed at 9,207 kb. The restriction patterns are shown in Table 1. The resulting eight fragments, from 103 kb to 2,322 kb, roughly corresponded to the physical restriction patterns of the total DNA seen in PFGE analysis. This supports the structural integrity of the complete genome sequence.

Bottom Line:
A significantly high level of sequence conservation was detected in three regions on each genome.An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements.The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

ABSTRACTThe complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.